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- PDB-8yw1: Semliki Forest virus viron in complex with VLDLR -

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Basic information

Entry
Database: PDB / ID: 8yw1
TitleSemliki Forest virus viron in complex with VLDLR
Components
  • (Spike glycoprotein ...) x 3
  • Very low-density lipoprotein receptor
  • capsid protein, partial
KeywordsVIRAL PROTEIN / Semliki Forest virus / VLDLR
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway ...reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway / very-low-density lipoprotein particle / positive regulation of dendrite development / cargo receptor activity / lipid transport / dendrite morphogenesis / regulation of synapse assembly / apolipoprotein binding / cholesterol metabolic process / clathrin-coated pit / receptor-mediated endocytosis / VLDLR internalisation and degradation / memory / calcium-dependent protein binding / nervous system development / receptor complex / lysosomal membrane / calcium ion binding / glutamatergic synapse / signal transduction / membrane / plasma membrane
Similarity search - Function
: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
: / Very low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Semliki Forest virus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsWang, J. / Zheng, T. / Yang, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Semliki Forest virus at 3.02 Angstroms resolution
Authors: Zheng, T.
History
DepositionMar 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein E1
B: Spike glycoprotein E2
C: Very low-density lipoprotein receptor
D: capsid protein, partial
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E2
J: Spike glycoprotein E2
K: Spike glycoprotein E2
L: Spike glycoprotein E3
M: Spike glycoprotein E3
N: Spike glycoprotein E3
O: capsid protein, partial
P: capsid protein, partial
Q: capsid protein, partial
S: Spike glycoprotein E3
E: Spike glycoprotein E1
R: Spike glycoprotein E2
T: capsid protein, partial
U: Spike glycoprotein E1
V: Spike glycoprotein E1
W: Spike glycoprotein E1
X: Spike glycoprotein E2
Y: Spike glycoprotein E2
Z: Spike glycoprotein E2
a: Spike glycoprotein E3
b: Spike glycoprotein E3
c: Spike glycoprotein E3
d: capsid protein, partial
e: capsid protein, partial
f: capsid protein, partial
g: Spike glycoprotein E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)967,94257
Polymers953,86533
Non-polymers14,07724
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Spike glycoprotein ... , 3 types, 24 molecules AFGHEUVWBIJKRXYZLMNSabcg

#1: Protein
Spike glycoprotein E1


Mass: 47489.766 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#2: Protein
Spike glycoprotein E2


Mass: 46468.867 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: Molecular name is based on https://www.ebi.ac.uk/interpro/protein/UniProt/A0A0E3T652/ as Uniprot Reference A0A0E3T652 and author provided name are both Structural polyprotein.
Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#5: Protein
Spike glycoprotein E3


Mass: 5848.729 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652

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Protein , 2 types, 9 molecules CDOPQTdef

#3: Protein Very low-density lipoprotein receptor / VLDL receptor / VLDL-R


Mass: 13075.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Production host: Homo sapiens (human) / References: UniProt: P98155
#4: Protein
capsid protein, partial


Mass: 17791.299 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652

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Sugars , 1 types, 24 molecules

#6: Polysaccharide...
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 24 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Semliki Forest virus viron in complex with VLDLR-LA3-5
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Semliki Forest virus 4
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44701 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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